Submitted to: Virology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 5/22/2009
Publication Date: 6/28/2009
Publication URL: handle.nal.usda.gov/10113/41352
Citation: Miller, P.J., Kim, L.M., Afonso, C.L., Ip, H.S. 2009. Evolutionary dynamics of Newcastle disease virus. Virology. 391:64-72. Interpretive Summary: Outbreaks of Newcastle disease (ND) in Ireland (1990) and Australia (1998-2000) were caused by endemic Newcastle disease viruses (NDV) originally of low virulence, circulating in wild birds in Ireland and in poultry in Australia, that changed from causing little to no disease in poultry to being able to cause severe mortality in poultry. While most endemic NDV in the United States (U.S.) are of low virulence, causing only sub-clinical or mild respiratory disease, the possibility that these viruses could develop increased virulence upon replication in poultry is a cause for concern. This risk is highlighted by 1) laboratory studies demonstrating that NDV originally was unable to produce disease in chickens are able to cause severe disease after multiple passages in chickens and 2) recent studies demonstrating the existence of many lineages of endemic NDV in live bird markets, waterfowl and shorebirds in the U.S., the type and numbers of which were previously unknown. Despite this risk, few studies provide insights into the evolutionary mechanisms affecting genomic changes. Here we explored the role of the evolutionary forces of recombination, negative and positive selection, and virulence of the cleavage site on the evolutionary changes of NDV proteins. While NDV are able to recombine and produce progeny that are combinations of multiple viruses, allowing the genomes of these progeny NDV to be vastly different from other circulating NDV, we found that recombination in nature happens infrequently. After evaluating large numbers of NDV sequences isolated over many years that had been deposited in GenBank, we found that virulent NDV had more changes in their fusion protein gene in a year than the NDV of low virulence. The majority of the NDV genome, including the cleavage site that determines virulence, was under negative selection, which maintains the genome, not positive selection, which favors changes in the genome.
Technical Abstract: A comprehensive dataset of Newcastle disease viruses (NDV) genome sequences was evaluated using bioinformatics to characterize the evolutionary forces affecting NDV genomes. Despite evidence of recombination in most genes, only one event in the fusion gene of genotype V viruses produced evolutionarily viable progenies. The codon-associated rate of change for the six NDV proteins revealed that the highest rate of change occurred at the fusion protein. All proteins were under strong purifying (negative) selection the fusion protein displayed the highest number of amino acids under positive selection. Regardless of the phylogenetic grouping or the level of virulence, the cleavage site motif was highly conserved implying that mutations resulting in changes of virulence may not be favored during NDV evolution. The coding sequence of the fusion gene and the genomes of viruses from wild birds displayed higher yearly rates of change in virulent viruses than in viruses of low virulence, suggesting that virulence may accelerate the rate of NDV evolution.